Dear Christoph, Thank you for your kind answers. I know that Lammps can handle nm and KJ/mol dependent on the unit setting in Lammps.
I have one more question about csg_fmatch. Does this command also use KJ/mol and KJ/mol-nm because I analysed Gromacs trajectory? Thank you. Best regards, Changwoon Jang On Tue, Dec 22, 2015 at 7:14 PM, Christoph Junghans <[email protected]> wrote: > 2015-12-22 16:53 GMT-07:00 Chang Woon Jang <[email protected]>: > > Dear Christoph, > > > > I mean the file written by csg_boltzmann with Tab command. If > > csg_boltzmann used GROMACS units, I think the second column (energy) in > > KJ/mol, and the third column (force) in KJ/mol-nm. Am I right? > Correct! (Assuming your input was in nm). > > > > > In lammps I will use, the energy should be Kcal/mol and the force should > be > > Kcal/mol-Angstrom. > And again lammps can use nm and KJ/mol, too. > > Christoph > > > > > Therefore, I would like to make sure that the file units from > csg_boltzmann > > Tab use KJ/mol and KJ/mol-nm. > > > > If I am wrong, please correct me. > > > > Thank you. > > > > Best regards, > > Changwoon Jang > > > > > > On Tue, Dec 22, 2015 at 6:30 PM, Christoph Junghans <[email protected]> > > wrote: > >> > >> 2015-12-22 15:56 GMT-07:00 Chang Woon Jang <[email protected]>: > >> > Dear Christoph, > >> > > >> > Thank you, Christoph. I have one more question. I ran an atomistic > >> > simulation in GROMACS. > >> > > >> > Are the units written in the file KJ/mol and KJ/mol-nm for energy and > >> > force, > >> > respectively? > >> Yes & no, csg_boltzmann uses Gromacs units. > >> While csg_inverse uses nm and the rest depends on what you use for > >> k_B*T in the settings file. > >> > >> However, lammps can do simulation in nm as well, see the > >> spce/ibi_lammps example: > >> <https://github.com/votca/csg-tutorials/tree/master/spce/ibi_lammps> > >> > >> Christoph > >> > > >> > I need to convert and format the energy and force for Lammps > simulation. > >> > > >> > Thank you. > >> > > >> > Best regards, > >> > Changwoon Jang > >> > > >> > > >> > On Tue, Dec 22, 2015 at 5:44 PM, Christoph Junghans < > [email protected]> > >> > wrote: > >> >> > >> >> 2015-12-22 15:04 GMT-07:00 Chang Woon Jang <[email protected] > >: > >> >> > Dear Votca Users, > >> >> > > >> >> > I have used csg_boltzmann with "tab" command to write the > >> >> > Boltzmann-inverted potential. > >> >> > > >> >> > It gives three columns. In the manual, the format of the file is > >> >> > described > >> >> > in sec 3.6. It states that "Those tables generally have the format > >> >> > > >> >> > x y [error] flag > >> >> > > >> >> > where x is input quantity (e.g. radius, angle), y is the computed > >> >> > quantity > >> >> > (e.g. a potential) and [error] is an optional error for y." > >> >> > > >> >> > However, I do not believe that the third column is error because > when > >> >> > I > >> >> > draw > >> >> > the third column as a function of radius (the first column) is much > >> >> > much > >> >> > bigger than the second column. Also, there is no flag. > >> >> > > >> >> > Is this still correct format of Boltzmann-inverted potential file > >> >> > from > >> >> > Tab > >> >> > command of csg_boltzmann as described in Votca Manual? > >> >> csg_boltzmann uses a different format for table than csg_inverse > (sec. > >> >> 3.6). > >> >> csg_boltzmann writes the force in 3rd column. > >> >> > >> >> Cheers, > >> >> > >> >> Christoph > >> >> > > >> >> > I attached the figure for you. > >> >> > > >> >> > -- > >> >> > Best regards, > >> >> > Changwoon Jang, > >> >> > > >> >> > -- > >> >> > You received this message because you are subscribed to the Google > >> >> > Groups > >> >> > "votca" group. > >> >> > To unsubscribe from this group and stop receiving emails from it, > >> >> > send > >> >> > an > >> >> > email to [email protected]. > >> >> > To post to this group, send email to [email protected]. > >> >> > Visit this group at https://groups.google.com/group/votca. > >> >> > For more options, visit https://groups.google.com/d/optout. > >> >> > >> >> > >> >> > >> >> -- > >> >> Christoph Junghans > >> >> Web: http://www.compphys.de > >> >> > >> >> -- > >> >> You received this message because you are subscribed to the Google > >> >> Groups > >> >> "votca" group. > >> >> To unsubscribe from this group and stop receiving emails from it, > send > >> >> an > >> >> email to [email protected]. > >> >> To post to this group, send email to [email protected]. > >> >> Visit this group at https://groups.google.com/group/votca. > >> >> For more options, visit https://groups.google.com/d/optout. > >> > > >> > -- > >> > You received this message because you are subscribed to the Google > >> > Groups > >> > "votca" group. > >> > To unsubscribe from this group and stop receiving emails from it, send > >> > an > >> > email to [email protected]. > >> > To post to this group, send email to [email protected]. > >> > Visit this group at https://groups.google.com/group/votca. > >> > For more options, visit https://groups.google.com/d/optout. > >> > >> > >> > >> -- > >> Christoph Junghans > >> Web: http://www.compphys.de > >> > >> -- > >> You received this message because you are subscribed to the Google > Groups > >> "votca" group. > >> To unsubscribe from this group and stop receiving emails from it, send > an > >> email to [email protected]. > >> To post to this group, send email to [email protected]. > >> Visit this group at https://groups.google.com/group/votca. > >> For more options, visit https://groups.google.com/d/optout. > > > > > > -- > > You received this message because you are subscribed to the Google Groups > > "votca" group. > > To unsubscribe from this group and stop receiving emails from it, send an > > email to [email protected]. > > To post to this group, send email to [email protected]. > > Visit this group at https://groups.google.com/group/votca. > > For more options, visit https://groups.google.com/d/optout. > > > > -- > Christoph Junghans > Web: http://www.compphys.de > > -- > You received this message because you are subscribed to the Google Groups > "votca" group. > To unsubscribe from this group and stop receiving emails from it, send an > email to [email protected]. > To post to this group, send email to [email protected]. > Visit this group at https://groups.google.com/group/votca. > For more options, visit https://groups.google.com/d/optout. > -- You received this message because you are subscribed to the Google Groups "votca" group. 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